Dataset Information

Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.

ABSTRACT: Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.

SUBMITTER: Stark Z

PROVIDER: S-EPMC8456155 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.

Stark Zornitza Z Foulger Rebecca E RE Williams Eleanor E Thompson Bryony A BA Patel Chirag C Lunke Sebastian S Snow Catherine C Leong Ivone U S IUS Puzriakova Arina A Daugherty Louise C LC Leigh Sarah S Boustred Christopher C Niblock Olivia O Rueda-Martin Antonio A Gerasimenko Oleg O Savage Kevin K Bellamy William W Lin Victor San Kho VSK Valls Roman R Gordon Lavinia L Brittain Helen K HK Thomas Ellen R A ERA Taylor Tavares Ana Lisa AL McEntagart Meriel M White Susan M SM Tan Tiong Y TY Yeung Alison A Downie Lilian L Macciocca Ivan I Savva Elena E Lee Crystle C Roesley Ain A De Fazio Paul P Deller Jane J Deans Zandra C ZC Hill Sue L SL Caulfield Mark J MJ North Kathryn N KN Scott Richard H RH Rendon Augusto A Hofmann Oliver O McDonagh Ellen M EM

American journal of human genetics 20210729 9

Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene ...[more]

PMID: 34329581

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Project description:ImportanceCancer screening deficits during the first year of the COVID-19 pandemic were found to persist into 2021. Cancer-related deaths over the next decade are projected to increase if these deficits are not addressed.ObjectiveTo assess whether participation in a nationwide quality improvement (QI) collaborative, Return-to-Screening, was associated with restoration of cancer screening.Design, setting, and participantsAccredited cancer programs electively enrolled in this QI study. Project-specific targets were established on the basis of differences in mean monthly screening test volumes (MTVs) between representative prepandemic (September 2019 and January 2020) and pandemic (September 2020 and January 2021) periods to restore prepandemic volumes and achieve a minimum of 10% increase in MTV. Local QI teams implemented evidence-based screening interventions from June to November 2021 (intervention period), iteratively adjusting interventions according to their MTVs and target. Interrupted time series analyses was used to identify the intervention effect. Data analysis was performed from January to April 2022.ExposuresCollaborative QI support included provision of a Return-to-Screening plan-do-study-act protocol, evidence-based screening interventions, QI education, programmatic coordination, and calculation of screening deficits and targets.Main outcomes and measuresThe primary outcome was the proportion of QI projects reaching target MTV and counterfactual differences in the aggregate number of screening tests across time periods.ResultsOf 859 cancer screening QI projects (452 for breast cancer, 134 for colorectal cancer, 244 for lung cancer, and 29 for cervical cancer) conducted by 786 accredited cancer programs, 676 projects (79%) reached their target MTV. There were no hospital characteristics associated with increased likelihood of reaching target MTV except for disease site (lung vs breast, odds ratio, 2.8; 95% CI, 1.7 to 4.7). During the preintervention period (April to May 2021), there was a decrease in the mean MTV (slope, -13.1 tests per month; 95% CI, -23.1 to -3.2 tests per month). Interventions were associated with a significant immediate (slope, 101.0 tests per month; 95% CI, 49.1 to 153.0 tests per month) and sustained (slope, 36.3 tests per month; 95% CI, 5.3 to 67.3 tests per month) increase in MTVs relative to the preintervention trends. Additional screening tests were performed during the intervention period compared with the prepandemic period (170 748 tests), the pandemic period (210 450 tests), and the preintervention period (722 427 tests).Conclusions and relevanceIn this QI study, participation in a national Return-to-Screening collaborative with a multifaceted QI intervention was associated with improvements in cancer screening. Future collaborative QI endeavors leveraging accreditation infrastructure may help address other gaps in cancer care.

Dataset Information

Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.

Publications

Scaling national and international improvement in virtual gene panel curation via a collaborative approach to discordance resolution.

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